Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Z6G8N

Calculation Name: 5E38-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5E38

Chain ID: A

ChEMBL ID:

UniProt ID: P9WFF3

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 211
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2183192.920978
FMO2-HF: Nuclear repulsion 2105598.784041
FMO2-HF: Total energy -77594.136938
FMO2-MP2: Total energy -77821.448563


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-6:GLY)


Summations of interaction energy for fragment #1(A:-6:GLY)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-14.038-8.4210.806-3.031-3.3930.001
Interaction energy analysis for fragmet #1(A:-6:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.006
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A-4ALA00.0420.0063.785-0.5391.299-0.015-1.060-0.7630.006
4A-3PHE0-0.015-0.0016.645-0.065-0.0650.0000.0000.0000.000
5A-2GLN00.0380.02710.3200.0520.0520.0000.0000.0000.000
6A-1GLY0-0.0650.06113.8030.0630.0630.0000.0000.0000.000
7A0ALA0-0.002-0.10717.2940.0130.0130.0000.0000.0000.000
8A1VAL0-0.0020.01116.0200.0160.0160.0000.0000.0000.000
9A2GLN0-0.031-0.01214.729-0.090-0.0900.0000.0000.0000.000
10A3VAL00.0490.00412.532-0.046-0.0460.0000.0000.0000.000
11A4HIS0-0.053-0.0268.6560.0740.0740.0000.0000.0000.000
12A5VAL0-0.019-0.0077.7840.1230.1230.0000.0000.0000.000
13A6VAL0-0.011-0.0034.125-0.973-0.883-0.001-0.034-0.0550.000
14A7ASP-1-0.915-0.9463.492-0.463-0.0130.009-0.127-0.3330.000
15A8HIS00.0340.0182.374-0.8200.9660.683-0.932-1.5370.002
16A9PRO00.0260.0043.902-0.1610.0150.005-0.035-0.1460.000
17A10LEU0-0.022-0.0196.844-0.284-0.2840.0000.0000.0000.000
18A11ALA00.0780.0336.344-0.017-0.0170.0000.0000.0000.000
19A12ALA00.0730.0397.7460.0980.0980.0000.0000.0000.000
20A13ALA0-0.044-0.0059.4360.0860.0860.0000.0000.0000.000
21A14ARG10.9250.96211.2240.1240.1240.0000.0000.0000.000
22A15LEU00.0830.08611.8230.0580.0580.0000.0000.0000.000
23A16THR0-0.059-0.06313.1960.0560.0560.0000.0000.0000.000
24A17THR0-0.141-0.12115.5140.0340.0340.0000.0000.0000.000
25A18LEU00.0080.00715.0010.0190.0190.0000.0000.0000.000
26A19ARG10.8940.93615.0680.4350.4350.0000.0000.0000.000
27A20ASP-1-0.851-0.90819.846-0.065-0.0650.0000.0000.0000.000
28A21GLU-1-0.890-0.93121.934-0.111-0.1110.0000.0000.0000.000
29A22ARG10.7880.87623.0080.0570.0570.0000.0000.0000.000
30A23THR0-0.077-0.01921.4330.0110.0110.0000.0000.0000.000
31A24ASP-1-0.824-0.90824.710-0.077-0.0770.0000.0000.0000.000
32A25ASN00.0570.01524.825-0.010-0.0100.0000.0000.0000.000
33A26ALA0-0.045-0.01424.665-0.015-0.0150.0000.0000.0000.000
34A27GLY00.0330.01022.486-0.007-0.0070.0000.0000.0000.000
35A28PHE00.0110.01720.647-0.016-0.0160.0000.0000.0000.000
36A29ARG10.9580.96520.0670.1100.1100.0000.0000.0000.000
37A30ALA0-0.076-0.03220.176-0.016-0.0160.0000.0000.0000.000
38A31ALA0-0.046-0.01716.603-0.005-0.0050.0000.0000.0000.000
39A32LEU00.0240.00615.369-0.056-0.0560.0000.0000.0000.000
40A33ARG10.9300.96515.7490.1030.1030.0000.0000.0000.000
41A34GLU-1-0.877-0.93513.288-0.225-0.2250.0000.0000.0000.000
42A35LEU0-0.051-0.0239.770-0.070-0.0700.0000.0000.0000.000
43A36THR00.004-0.00711.303-0.194-0.1940.0000.0000.0000.000
44A37LEU00.0780.05311.279-0.141-0.1410.0000.0000.0000.000
45A38LEU0-0.089-0.0267.170-0.103-0.1030.0000.0000.0000.000
46A39LEU00.0020.0017.858-0.437-0.4370.0000.0000.0000.000
47A40ILE00.0420.0239.691-0.068-0.0680.0000.0000.0000.000
48A41TYR0-0.053-0.0246.5770.1730.1730.0000.0000.0000.000
49A42GLU-1-0.930-0.9833.119-9.757-8.4800.125-0.843-0.559-0.007
50A43ALA0-0.027-0.0017.4430.1380.1380.0000.0000.0000.000
51A44THR0-0.065-0.03410.8850.2240.2240.0000.0000.0000.000
52A45ARG10.9050.9696.2311.7581.7580.0000.0000.0000.000
53A46ASP-1-0.904-0.95411.050-0.561-0.5610.0000.0000.0000.000
54A47ALA00.0960.02714.7430.0210.0210.0000.0000.0000.000
55A48PRO0-0.0310.02216.5530.0360.0360.0000.0000.0000.000
56A49CYS0-0.109-0.07719.4340.0370.0370.0000.0000.0000.000
57A50GLU-1-0.894-0.96022.240-0.108-0.1080.0000.0000.0000.000
58A51PRO0-0.046-0.02624.1060.0060.0060.0000.0000.0000.000
59A52VAL0-0.0010.00725.424-0.006-0.0060.0000.0000.0000.000
60A53PRO0-0.0080.00328.0020.0120.0120.0000.0000.0000.000
61A54ILE0-0.005-0.00427.427-0.005-0.0050.0000.0000.0000.000
62A55ARG10.9160.94331.400-0.004-0.0040.0000.0000.0000.000
63A56THR0-0.0150.02830.087-0.002-0.0020.0000.0000.0000.000
64A57PRO00.021-0.01731.946-0.002-0.0020.0000.0000.0000.000
65A58LEU0-0.054-0.02332.8220.0000.0000.0000.0000.0000.000
66A59ALA00.0200.01434.0260.0040.0040.0000.0000.0000.000
67A60GLU-1-0.903-0.96333.6230.0130.0130.0000.0000.0000.000
68A61THR0-0.028-0.01628.3650.0050.0050.0000.0000.0000.000
69A62VAL00.0080.00026.940-0.009-0.0090.0000.0000.0000.000
70A63GLY0-0.0180.00324.6000.0130.0130.0000.0000.0000.000
71A64SER0-0.028-0.00820.4350.0030.0030.0000.0000.0000.000
72A65ARG10.9710.97221.8660.0970.0970.0000.0000.0000.000
73A66LEU00.0210.01917.6350.0030.0030.0000.0000.0000.000
74A67THR0-0.0450.00221.1850.0120.0120.0000.0000.0000.000
75A68LYS10.9400.95321.9470.1770.1770.0000.0000.0000.000
76A69PRO00.0220.01921.203-0.027-0.0270.0000.0000.0000.000
77A70PRO00.0010.00518.5870.0120.0120.0000.0000.0000.000
78A71LEU00.0160.01521.5720.0180.0180.0000.0000.0000.000
79A72LEU0-0.014-0.01319.126-0.039-0.0390.0000.0000.0000.000
80A73VAL00.0300.00322.0390.0340.0340.0000.0000.0000.000
81A74PRO0-0.0130.00222.542-0.026-0.0260.0000.0000.0000.000
82A75VAL00.0020.01523.0730.0330.0330.0000.0000.0000.000
83A76LEU0-0.0300.00725.0910.0000.0000.0000.0000.0000.000
84A77ARG10.9510.93427.8750.1910.1910.0000.0000.0000.000
85A78ALA0-0.0060.00423.5730.0060.0060.0000.0000.0000.000
86A79GLY00.0700.01721.554-0.003-0.0030.0000.0000.0000.000
87A80LEU0-0.026-0.01722.139-0.008-0.0080.0000.0000.0000.000
88A81GLY0-0.0020.00522.3010.0160.0160.0000.0000.0000.000
89A82MET0-0.037-0.01116.0480.0170.0170.0000.0000.0000.000
90A83VAL00.0400.01619.003-0.013-0.0130.0000.0000.0000.000
91A84ASP-1-0.973-0.98621.413-0.155-0.1550.0000.0000.0000.000
92A85GLU-1-0.911-0.95815.820-0.331-0.3310.0000.0000.0000.000
93A86ALA00.0620.02917.287-0.007-0.0070.0000.0000.0000.000
94A87HIS00.0020.00718.3320.0000.0000.0000.0000.0000.000
95A88ALA0-0.027-0.00718.6170.0210.0210.0000.0000.0000.000
96A89ALA0-0.036-0.01415.1640.0190.0190.0000.0000.0000.000
97A90LEU0-0.077-0.04716.2700.0120.0120.0000.0000.0000.000
98A91PRO00.0120.01219.4840.0060.0060.0000.0000.0000.000
99A92GLU-1-0.958-0.99922.942-0.125-0.1250.0000.0000.0000.000
100A93ALA0-0.0410.00521.5150.0010.0010.0000.0000.0000.000
101A94HIS00.0000.01023.6250.0100.0100.0000.0000.0000.000
102A95VAL0-0.006-0.01524.556-0.025-0.0250.0000.0000.0000.000
103A96GLY00.0070.01126.2940.0200.0200.0000.0000.0000.000
104A97PHE0-0.032-0.02026.902-0.020-0.0200.0000.0000.0000.000
105A98DVA00.0240.00328.7770.0120.0120.0000.0000.0000.000
106A99GLY0-0.065-0.01828.572-0.019-0.0190.0000.0000.0000.000
107A100VAL0-0.044-0.00329.2000.0120.0120.0000.0000.0000.000
108A101DAL0-0.005-0.00229.581-0.011-0.0110.0000.0000.0000.000
109A102ARG10.8710.91027.9830.2150.2150.0000.0000.0000.000
110A103ASP-1-0.879-0.93132.297-0.143-0.1430.0000.0000.0000.000
111A104GLU-1-0.907-0.94634.948-0.135-0.1350.0000.0000.0000.000
112A105GLN0-0.017-0.01536.392-0.001-0.0010.0000.0000.0000.000
113A106THR0-0.066-0.03937.383-0.008-0.0080.0000.0000.0000.000
114A107HIS00.0220.00430.157-0.008-0.0080.0000.0000.0000.000
115A108GLN0-0.044-0.00533.982-0.015-0.0150.0000.0000.0000.000
116A109PRO0-0.0030.01331.3960.0060.0060.0000.0000.0000.000
117A110VAL00.0340.01633.8840.0020.0020.0000.0000.0000.000
118A111PRO0-0.0080.00834.108-0.004-0.0040.0000.0000.0000.000
119A112DTY0-0.049-0.03834.3410.0140.0140.0000.0000.0000.000
120A113DLE0-0.035-0.04034.296-0.007-0.0070.0000.0000.0000.000
121A114DAS-1-0.875-0.94033.055-0.170-0.1700.0000.0000.0000.000
122A115DSN0-0.044-0.01632.8920.0060.0060.0000.0000.0000.000
123A116LEU00.0370.01729.376-0.013-0.0130.0000.0000.0000.000
124A117PRO0-0.062-0.03829.8280.0110.0110.0000.0000.0000.000
125A118DAS-1-0.914-0.96932.626-0.134-0.1340.0000.0000.0000.000
126A119ASP-1-0.915-0.94529.170-0.228-0.2280.0000.0000.0000.000
127A120LEU0-0.006-0.02131.8620.0090.0090.0000.0000.0000.000
128A121THR0-0.042-0.03829.222-0.006-0.0060.0000.0000.0000.000
129A122ASP-1-0.904-0.93827.229-0.212-0.2120.0000.0000.0000.000
130A123VAL0-0.080-0.05825.6650.0050.0050.0000.0000.0000.000
131A124PRO00.0320.04120.482-0.009-0.0090.0000.0000.0000.000
132A125VAL00.0330.00921.6820.0150.0150.0000.0000.0000.000
133A126MET0-0.040-0.02014.244-0.067-0.0670.0000.0000.0000.000
134A127VAL00.0110.00819.1560.0290.0290.0000.0000.0000.000
135A128LEU0-0.013-0.00317.316-0.074-0.0740.0000.0000.0000.000
136A129ASP-1-0.848-0.95918.754-0.324-0.3240.0000.0000.0000.000
137A130PRO00.0170.01217.847-0.057-0.0570.0000.0000.0000.000
138A131MET0-0.0130.00918.017-0.040-0.0400.0000.0000.0000.000
139A132VAL00.0540.04318.8030.0400.0400.0000.0000.0000.000
140A133ALA00.032-0.00321.030-0.011-0.0110.0000.0000.0000.000
141A134THR00.0500.00323.772-0.007-0.0070.0000.0000.0000.000
142A135GLY00.0700.03624.993-0.003-0.0030.0000.0000.0000.000
143A136GLY0-0.0210.04425.9610.0020.0020.0000.0000.0000.000
144A137SER00.0510.01726.3020.0050.0050.0000.0000.0000.000
145A138MET00.0180.02921.2050.0080.0080.0000.0000.0000.000
146A139THR0-0.002-0.06725.2640.0130.0130.0000.0000.0000.000
147A140HIS00.0120.01527.5940.0250.0250.0000.0000.0000.000
148A141THR00.006-0.00325.9300.0130.0130.0000.0000.0000.000
149A142LEU00.006-0.01722.8940.0070.0070.0000.0000.0000.000
150A143GLY0-0.015-0.00227.1960.0070.0070.0000.0000.0000.000
151A144LEU00.003-0.00530.4970.0120.0120.0000.0000.0000.000
152A145LEU00.0140.04325.1740.0050.0050.0000.0000.0000.000
153A146ILE0-0.035-0.00828.1660.0080.0080.0000.0000.0000.000
154A147SER0-0.120-0.08029.9600.0150.0150.0000.0000.0000.000
155A148ARG0-0.088-0.04032.0700.0160.0160.0000.0000.0000.000
156A149GLY0-0.0060.01131.5950.0000.0000.0000.0000.0000.000
157A150ALA00.0750.05426.193-0.002-0.0020.0000.0000.0000.000
158A151ALA00.006-0.00125.305-0.004-0.0040.0000.0000.0000.000
159A152ASP-1-1.003-0.98319.530-0.445-0.4450.0000.0000.0000.000
160A153ILE00.0440.01120.9960.0010.0010.0000.0000.0000.000
161A154THR0-0.015-0.00314.532-0.065-0.0650.0000.0000.0000.000
162A155VAL0-0.008-0.00616.7720.0640.0640.0000.0000.0000.000
163A156LEU0-0.015-0.00812.626-0.129-0.1290.0000.0000.0000.000
164A157CYS0-0.069-0.03314.2000.0870.0870.0000.0000.0000.000
165A158VAL0-0.027-0.01213.560-0.140-0.1400.0000.0000.0000.000
166A159VAL00.0230.01513.774-0.091-0.0910.0000.0000.0000.000
167A160ALA0-0.0040.00316.1100.0420.0420.0000.0000.0000.000
168A161ALA00.0130.01217.774-0.008-0.0080.0000.0000.0000.000
169A162PRO00.0320.00919.958-0.023-0.0230.0000.0000.0000.000
170A163GLU-1-0.857-0.94321.264-0.294-0.2940.0000.0000.0000.000
171A164GLY00.0450.03322.5380.0130.0130.0000.0000.0000.000
172A165ILE0-0.006-0.01916.7960.0000.0000.0000.0000.0000.000
173A166ALA0-0.049-0.01620.9030.0100.0100.0000.0000.0000.000
174A167ALA0-0.027-0.01524.0640.0170.0170.0000.0000.0000.000
175A168LEU00.0080.01019.5110.0150.0150.0000.0000.0000.000
176A169GLN00.0480.03420.331-0.029-0.0290.0000.0000.0000.000
177A170LYS10.8810.94224.0850.2550.2550.0000.0000.0000.000
178A171ALA0-0.0070.01026.6400.0220.0220.0000.0000.0000.000
179A172ALA00.024-0.00424.6730.0170.0170.0000.0000.0000.000
180A173PRO0-0.048-0.03123.767-0.034-0.0340.0000.0000.0000.000
181A174ASN0-0.015-0.00522.150-0.020-0.0200.0000.0000.0000.000
182A175VAL0-0.0110.02119.513-0.022-0.0220.0000.0000.0000.000
183A176ARG10.8900.92412.6430.8280.8280.0000.0000.0000.000
184A177LEU0-0.010-0.00214.9040.0340.0340.0000.0000.0000.000
185A178PHE0-0.004-0.0108.794-0.130-0.1300.0000.0000.0000.000
186A179THR0-0.012-0.01411.3560.1520.1520.0000.0000.0000.000
187A180ALA00.0280.0079.392-0.391-0.3910.0000.0000.0000.000
188A181ALA0-0.023-0.0149.808-0.043-0.0430.0000.0000.0000.000
189A182ILE0-0.038-0.01212.2000.0450.0450.0000.0000.0000.000
190A183ASP-1-0.795-0.89314.839-0.433-0.4330.0000.0000.0000.000
191A184GLU-1-0.963-0.99217.852-0.240-0.2400.0000.0000.0000.000
192A185GLY00.008-0.00721.041-0.002-0.0020.0000.0000.0000.000
193A186LEU0-0.076-0.00723.190-0.004-0.0040.0000.0000.0000.000
194A187ASN00.0690.04026.0840.0010.0010.0000.0000.0000.000
195A188GLU-1-0.932-0.96529.177-0.148-0.1480.0000.0000.0000.000
196A189VAL0-0.0120.00231.1180.0010.0010.0000.0000.0000.000
197A190ALA0-0.033-0.02729.078-0.007-0.0070.0000.0000.0000.000
198A191TYR0-0.024-0.02326.612-0.019-0.0190.0000.0000.0000.000
199A192ILE0-0.016-0.01120.2850.0040.0040.0000.0000.0000.000
200A193VAL0-0.032-0.00623.4070.0100.0100.0000.0000.0000.000
201A194PRO00.016-0.01119.360-0.011-0.0110.0000.0000.0000.000
202A195GLY0-0.0070.00419.7120.0170.0170.0000.0000.0000.000
203A196LEU0-0.002-0.01117.8060.0080.0080.0000.0000.0000.000
204A197GLY00.0200.02021.7920.0290.0290.0000.0000.0000.000
205A198ASP-1-0.822-0.93424.611-0.246-0.2460.0000.0000.0000.000
206A199ALA00.0700.02421.9570.0080.0080.0000.0000.0000.000
207A200GLY0-0.073-0.00323.7600.0050.0050.0000.0000.0000.000
208A201ASP-1-0.808-0.89526.601-0.153-0.1530.0000.0000.0000.000
209A202ARG10.7830.89023.8250.2100.2100.0000.0000.0000.000
210A203GLN0-0.124-0.10823.5600.0010.0010.0000.0000.0000.000
211A204PHE0-0.046-0.01426.1230.0200.0200.0000.0000.0000.000